Search results for "Abstract"
showing 10 items of 1959 documents
The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis
2021
Abstract Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either mi…
Stochastic labelling of biological images
1998
Many hypotheses made by experimental researchers can be formulated as a stochastic labelling of a given image. Some stochastic labelling methods for random closed sets are proposed in this paper. Molchanov (I. Molchanov, 1984, Theor. Probability and Math. Statist.29, 113–119) provided the probabilistic background for this problem. However, there is a lack of specific labelling models. Ayala and Simo (G. Ayala and A. Simo, 1995, Advances in Applied Probability27, 293–305) proposed a method in which, given the whole set of connected components, every component is classified in a certain phase or category in a completely random way. Alternative methods are necessary in case the random labellin…
Investigation of Simulated Trading — A multi agent based trading system for optimization purposes
2010
Abstract Some years ago, Bachem, Hochstattler, and Malich proposed a heuristic algorithm called Simulated Trading for the optimization of vehicle routing problems. Computational agents place buy-orders and sell-orders for customers to be handled at a virtual financial market, the prices of the orders depending on the costs of inserting the customer in the tour or for his removal. According to a proposed rule set, the financial market creates a buy-and-sell graph for the various orders in the order book, intending to optimize the overall system. Here I present a thorough investigation for the application of this algorithm to the traveling salesman problem.
A tabu search algorithm for assigning teachers to courses
2002
In this paper we deal with the problem of assigning teachers to courses in a secondary school. The problem appears when a timetable is to be built and the teaching assignments are not fixed. We have developed a tabu search algorithm to solve the problem. The parameters involved in the algorithm have been estimated by using multiple regression techniques. The computational results, obtained on a set of Spanish secondary schools, show that the solutions obtained by this automatic procedure can be favourably compared with the solutions proposed by the experts.
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences
2015
Abstract Motivation: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. Results: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are inc…
Design-based estimation for geometric quantiles with application to outlier detection
2010
Geometric quantiles are investigated using data collected from a complex survey. Geometric quantiles are an extension of univariate quantiles in a multivariate set-up that uses the geometry of multivariate data clouds. A very important application of geometric quantiles is the detection of outliers in multivariate data by means of quantile contours. A design-based estimator of geometric quantiles is constructed and used to compute quantile contours in order to detect outliers in both multivariate data and survey sampling set-ups. An algorithm for computing geometric quantile estimates is also developed. Under broad assumptions, the asymptotic variance of the quantile estimator is derived an…
Segmented relationships to model erosion of regression effect in Cox regression
2010
In this article we propose a parsimonious parameterisation to model the so-called erosion of the covariate effect in the Cox model, namely a covariate effect approaching to zero as the follow-up time increases. The proposed parameterisation is based on the segmented relationship where proper constraints are set to accomodate for the erosion. Relevant hypothesis testing is discussed. The approach is illustrated on two historical datasets in the survival analysis literature, and some simulation studies are presented to show how the proposed framework leads to a test for a global effect with good power as compared with alternative procedures. Finally, possible generalisations are also present…
Efficient change point detection in genomic sequences of continuous measurements
2010
Abstract Motivation: Knowing the exact locations of multiple change points in genomic sequences serves several biological needs, for instance when data represent aCGH profiles and it is of interest to identify possibly damaged genes involved in cancer and other diseases. Only a few of the currently available methods deal explicitly with estimation of the number and location of change points, and moreover these methods may be somewhat vulnerable to deviations of model assumptions usually employed. Results: We present a computationally efficient method to obtain estimates of the number and location of the change points. The method is based on a simple transformation of data and it provides re…
Validity of the electroneutrality and goldman constant-field assumptions in describing the diffusion potential for ternary electrolyte systems in sim…
1986
Abstract Three numerical algorithms capable of simulating transport processes through simple, porous membranes in the steady state have been employed in order to study the change in the diffusion potential with the membrane thickness and the ionic concentrations for the ternary systems NaClHClH20 and CaCI2NaC1H 2 O. The first simulation procedure uses Poisson's equation, the two others replace this equation by the electroneutrality and Goldman constant-field approximations respectively. From the results presented here, conditions for the applicability of the electroneutrality and constantfield assumption to ternary electrolyte systems are given.
An algebraic representation of Steiner triple systems of order 13
2021
Abstract In this paper we construct an incidence structure isomorphic to a Steiner triple system of order 13 by defining a set B of twentysix vectors in the 13-dimensional vector space V = GF ( 5 ) 13 , with the property that there exist precisely thirteen 6-subsets of B whose elements sum up to zero in V , which can also be characterized as the intersections of B with thirteen linear hyperplanes of V .